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Horticultural crops are economically valuable for sustainable agricultural production. Plant diseases caused by Pathogens including virus, phytoplasma and bacterium have been a great threat to production of horticultural crops. The efficient use of pathogen-free plant materials has overcome the menace of plant diseases and has sustained crop production. Cryotherapy of shoot tips, a novel application of cryopreservation technique, has become a new plant biotechnology tool for plant pathogen eradication. When compared with the traditional methods, cryotherapy of shoot tips produces high frequency of pathogen-free plants, which is independent of shoot tip size and cryogenic methods. Cryotherapy of shoot tips has six major steps to produce pathogen-free plants: (1) introduction of infected plant materials into in vitro cultures; (2) excision of shoot tips; (3) cryotherapy; (4) post-culture for plant regeneration; (5) indexing of pathogens in regenerated plants after cryotherapy; and (6) establishment of pathogen-free nuclear stock plants. The key steps 2, 3, and 4 are similar to cryopreservation, and play a major role in obtaining high pathogen eradication frequency.